Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor
Quercitrin is an anti-lung cancer agent. It is a naturally occurring flavonoid and its derivatives are mainly present in nuts and beverages. It is mainly available as a glycoside, and the quercitrin glycosides are found to prevent the metastasis of cancer. Quercitrin is optimized with 6–311++G(d,p)...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-05-01
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| Series: | Heliyon |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2405844022008271 |
| _version_ | 1818209334931226624 |
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| author | M. Govindammal S. Kannan P. Srinivasan M. Prasath |
| author_facet | M. Govindammal S. Kannan P. Srinivasan M. Prasath |
| author_sort | M. Govindammal |
| collection | DOAJ |
| description | Quercitrin is an anti-lung cancer agent. It is a naturally occurring flavonoid and its derivatives are mainly present in nuts and beverages. It is mainly available as a glycoside, and the quercitrin glycosides are found to prevent the metastasis of cancer. Quercitrin is optimized with 6–311++G(d,p) basis set using the B3LYP method to attain its minimum energy structure. The vibrational studies of the Quercitrin compound were elucidated with reference to Potential Energy Distribution (PED). The geometrical parameters were obtained and correlated with experimental values. To examine the nature of the charge transfer mechanism of Quercitrin, the HOMO-LUMO energy gap is computed. The anti-cancer activity of Quercitrin has been explored using molecular docking study that are used to estimate how the ligand interacts with protein, specifically to identify the best-fit orientation of the ligand, its binding mode, and intermolecular interactions of amino acid residues in the binding region of B-RAF kinase protein. The binding affinity of the compound Quercitrin (-7.14 kcal/mol) was found using AutoDock and validated with a Glide XP score in Schrodinger tool (-8.01 kcal/mol). MD simulations of protein-ligand complexes were monitored for 100 ns, from which the RMSD, RMSF, Rg, H-bonds, and interaction energy calculations were executed. From these investigations, it is identified that the compound quercitrin has maintained good structural stability, compactness, higher Hydrogen bonds, and interaction energies than the Imidazopyridinyl benzamide inhibitor. |
| first_indexed | 2024-12-12T04:59:04Z |
| format | Article |
| id | doaj.art-cf223e2e053f4fca9c7af9a0ecfa6351 |
| institution | Directory Open Access Journal |
| issn | 2405-8440 |
| language | English |
| last_indexed | 2024-12-12T04:59:04Z |
| publishDate | 2022-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Heliyon |
| spelling | doaj.art-cf223e2e053f4fca9c7af9a0ecfa63512022-12-22T00:37:16ZengElsevierHeliyon2405-84402022-05-0185e09539Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitorM. Govindammal0S. Kannan1P. Srinivasan2M. Prasath3Department of Physics, Periyar University Centre for Post Graduate and Research Studies, Dharmapuri, 635 205, IndiaCentre for High Computing, CSIR-Central Leather Research Institute (CLRI), Chennai, 600020, IndiaChikkaiah Naicker College, Erode, 638004, IndiaDepartment of Physics, Periyar University Centre for Post Graduate and Research Studies, Dharmapuri, 635 205, India; Corresponding author.Quercitrin is an anti-lung cancer agent. It is a naturally occurring flavonoid and its derivatives are mainly present in nuts and beverages. It is mainly available as a glycoside, and the quercitrin glycosides are found to prevent the metastasis of cancer. Quercitrin is optimized with 6–311++G(d,p) basis set using the B3LYP method to attain its minimum energy structure. The vibrational studies of the Quercitrin compound were elucidated with reference to Potential Energy Distribution (PED). The geometrical parameters were obtained and correlated with experimental values. To examine the nature of the charge transfer mechanism of Quercitrin, the HOMO-LUMO energy gap is computed. The anti-cancer activity of Quercitrin has been explored using molecular docking study that are used to estimate how the ligand interacts with protein, specifically to identify the best-fit orientation of the ligand, its binding mode, and intermolecular interactions of amino acid residues in the binding region of B-RAF kinase protein. The binding affinity of the compound Quercitrin (-7.14 kcal/mol) was found using AutoDock and validated with a Glide XP score in Schrodinger tool (-8.01 kcal/mol). MD simulations of protein-ligand complexes were monitored for 100 ns, from which the RMSD, RMSF, Rg, H-bonds, and interaction energy calculations were executed. From these investigations, it is identified that the compound quercitrin has maintained good structural stability, compactness, higher Hydrogen bonds, and interaction energies than the Imidazopyridinyl benzamide inhibitor.http://www.sciencedirect.com/science/article/pii/S2405844022008271Lung cancerB-RAF kinaseDFT |
| spellingShingle | M. Govindammal S. Kannan P. Srinivasan M. Prasath Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor Heliyon Lung cancer B-RAF kinase DFT |
| title | Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor |
| title_full | Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor |
| title_fullStr | Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor |
| title_full_unstemmed | Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor |
| title_short | Quantum chemical calculations, spectroscopic studies and molecular docking investigations of the anti-cancer drug quercitrin with B-RAF inhibitor |
| title_sort | quantum chemical calculations spectroscopic studies and molecular docking investigations of the anti cancer drug quercitrin with b raf inhibitor |
| topic | Lung cancer B-RAF kinase DFT |
| url | http://www.sciencedirect.com/science/article/pii/S2405844022008271 |
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